jCO2 analysis
Ross Cunning
October 5, 2016
How many CO2’s can the host deliver to photosynthesis SU per 1 C-mol of fixed carbon? The host will use this carbon to generate ATP to energize the CO2-concentrating mechanisms that deliver CO2 to the photosynthesis SU.
Now remove feeding
##### VARY NITROGEN
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
defpars <- def_pars()
env <- init_env(time=time, L=c(15,15,2), N=c(1e-7,1e-6,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"),
c(40, 30, 1, 5, 0.9, 0.9, 0, 0)),
NPQ="fixed2")
plot_run_wC(run)
# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"),
c(40, 30, 1, 5, 0.9, 0.9, 0.32)),
NPQ="fixed2")
plot_run(run)
##### VARY LIGHT
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
env <- init_env(time=time, L=c(10,25,2), N=c(1e-7,1e-7,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"),
c(40, 30, 1, 5, 0.9, 0.9, 0, 0)),
NPQ="fixed2")
plot_run_wC(run)
# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"),
c(40, 30, 1, 5, 0.9, 0.9, 0.32)),
NPQ="fixed2")
plot_run(run)
Now make jPNQ inhibited
##### VARY NITROGEN
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
defpars <- def_pars()
env <- init_env(time=time, L=c(15,15,2), N=c(1e-7,1e-6,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"),
c(60, 40, 1, 5, 0.9, 0.9, 0, 0)),
NPQ="inhibited2")
plot_run_wC(run)
# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"),
c(60, 40, 1, 5, 0.9, 0.9, 0.32)),
NPQ="inhibited2")
plot_run(run)
##### VARY LIGHT
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,1)
env <- init_env(time=time, L=c(10,25,2), N=c(1e-7,1e-7,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"),
c(60, 40, 1, 5, 0.9, 0.9, 0, 0)),
NPQ="inhibited2")
plot_run_wC(run)
# RUN USING JCO2A (original version of model)
run <- run_coral(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a"),
c(60, 40, 1, 5, 0.9, 0.9, 0.32)),
NPQ="inhibited2")
plot_run(run)
Trying different stress parameter sets
##### VARY LIGHT
# RUN USING WASTED CARBON AND NO JCO2A OR JCO2P
time <- seq(1,1230,0.5)
env <- init_env(time=time, L=c(10,40,2), N=c(1e-7,1e-7,2), X=c(0,0,0))
run <- run_coral_wC(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"),
c(80, 40, 1, 5, 0.9, 0.9, 0, 0)),
NPQ="fixed2")
plot_run_wC(run)
run <- run_coral_wC(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"),
c(80, 80, 1, 5, 0.9, 0.9, 0, 0)),
NPQ="fixed2")
plot_run_wC(run)
run <- run_coral_wC(time=time, env=env,
pars=replace(defpars,
c("kNPQ", "kROS", "k", "b", "sigmaCS", "sigmaCH", "jCO2a", "jCO2p"),
c(60, 60, 1, 5, 0.9, 0.9, 0, 0)),
NPQ="inhibited2")
plot_run_wC(run)
with(run, {
plot(time, 5*H$jCw)
})